Bone marrow‑derived mesenchymal stem cells (BMSCs) and adipose tissue‑derived mesenchymal stem cells (ADSCs) are able to differentiate into neuron‑like cells when exposed to small molecule compounds, however the specific differences in their neuronal differentiation abilities remain to be fully elucidated. The present study aimed to compare the neuronal differentiation abilities of BMSCs and ADSCs. BMSCs and ADSCs from the same Sprague Dawley rats were isolated and cultured for use. The proliferation capacity was revealed using a cell counting method. Following BMSCs and ADSCs induction by four types of small‑molecular compounds, the expression of various neuronal markers and the secretion of several neurotrophic factors were detected by immunofluorescence, western blotting, reverse transcription‑quantitative polymerase chain reaction and ELISA. It was demonstrated that the ADSCs exhibited an increased proliferation capacity compared with BMSCs, according to cumulative population doubling analyses. Following a 7‑day neuronal induction period, BMSCs and ADSCs exhibited a neuron‑like morphology, and were termed neuronal induced (NI)‑BMSCs and NI‑ADSCs. They expressed neuronal markers including β‑tubulin III, microtubule associated protein 2 and choline acetyltransferase. The number of NI‑BMSCs that positively expressed the neuronal markers was significantly decreased compared with NI‑ADSCs, and the expression and secretion of the neurotrophic factors nerve growth factor and 3'‑nucleotidase in NI‑BMSCs were additionally decreased compared with NI‑ADSCs. The findings of the present study indicated that the neuronal differentiation abilities and neurotrophic factor secretion abilities of ADSCs were increased compared with BMSCs. ADSCs may therefore act as efficient candidates in cell transplantation therapy for diseases and injuries of the nervous system.